A closed-door encounter between two college acquaintances. Both have been drinking. One says she was raped; the other insists it was consensual. There are no other witnesses.

It’s a common scenario in college sexual assault cases, and a potential nightmare to resolve. But under the 40-year-old federal gender equity law Title IX — and guidance handed down last year by the Obama administration on how to apply it — colleges can’t just turn such cases over to criminal prosecutors, who often won’t touch them anyway. Instead, they must investigate, and in campus proceedings do their best to balance the accused’s due process rights with the civil right of the victim to a safe education.

Lately, though, the legal ramifications of such cases are spilling off campus, with schools caught in the middle. Colleges that do too little about sexual assault could lose federal funds. The Department of Education’s Office of Civil Rights is currently investigating a dozen colleges and universities over their response to sexual violence (documents obtained under the Freedom of Information Act show schools that have recently agreed to take steps to resolve OCR complaints over Title IX policies include universities such as Notre Dame, Northwestern and George Washington).

Meanwhile, judgments in Title IX lawsuits against colleges, usually brought by accusers, are soaring. Compounding the fear: In some such cases, college administrators may be found personally liable.

But when colleges do take action against accused students, those students are increasingly lawyering up themselves, suing for breach of contract and negligence. And in at least two recent cases, in Tennessee and Massachusetts, male students have tread novel legal ground by alleging violations of their own Title IX protections against gender discrimination, arguing a college’s sexual assault policies or procedures were unfairly stacked against men.

Whether or not such Title IX arguments hold up, they underscore a new fact of life: For better or for worse, the days when colleges could count on handling such matters quietly behind closed doors are over.

A 1999 U.S. Supreme Court decision established potential liability under Title IX for schools that fail to address sexual harassment and, in its extreme form, sexual assault.

Now, Title IX cases represent “the most expensive lawsuits in history” against colleges, said Brett Sokolow, managing partner of the National Center for Higher Education Risk Management.

Among them: The University of Colorado faced a $2.85 million verdict under Title IX after two students were allegedly raped by football recruits and players at an off-campus recruiting event in 2001. An appeals court essentially held that Colorado had an official policy to show recruits “a good time,” which created a dangerous culture for sexual assaults. The jury verdict in a sports-related Title IX discrimination case at California State University-Fresno ran to $19.1 million, though that was later reduced to $6.6 million.

Such verdicts have cast a cloud of fear over college attorneys and administrators. Some advocates welcome that. They hope it will prompt long-overdue measures to ensure sexual assaults don’t deny women access to education.

But there are concerns of overreach.

In March, 2011, in a response to student protesters who had occupied a campus building and were calling for stronger policies to combat sexual assault, the president of Dickinson College in Pennsylvania announced that expulsion would be the only available sanction for rape.

Numerous experts and administrators at other campuses called such a policy unusual and troubling. They say it deprives educators of flexibility in handling cases that often aren’t black and white. And like any sentencing minimum, it may have the unintended effect of making conduct boards less likely to convict at all. (Dickinson dropped the policy in guidelines published last December, which refer more broadly to sexual assault, and standardize punishments ranging from one-year suspension to expulsion).

“It drives —not hysteria, that’s not the right word — but nearly that,” Sokolow said. “It’s such a fear-based reaction that a lot of colleges now are expelling and suspending people they shouldn’t, for fear they’ll get nailed on Title IX.”

Hans Bader, a former attorney with the Department of Education’s Office of Civil Rights, says campus conduct boards, fearing Title IX lawsuits, will inevitably err on the side of punishment.

“Innocent people get found guilty of harassment because the school realizes the only way it can avoid liability is to punish everybody in sight,” he said.

But that’s a legal danger, too. Students accused of sexual violence don’t buy the argument that such proceedings are merely “educational,” affecting nothing more than their academic standing.

“Fifteen years ago, 20 years ago, if a student got into trouble he would just drop out and go elsewhere,” Sokolow said. “Now colleges are starting to share information, they’re starting to put notations on transcripts.” With more at stake, “We’re seeing more students who want to stand and fight.”

Typically, such suits allege breach of contract or negligence, like a recently resolved high-profile case involving Brown University, brought by a former student who contended Brown rushed an investigation and caved to pressure from the accuser’s father, a prominent donor.

But recently, at least two have made an apparently novel argument citing the Title IX rights of accused male students. Their argument: Title IX, while requiring numerous protections for sexual assault victims, fundamentally concerns gender equity, and men can be victimized, too.

A federal judge threw out the Title IX claim brought by a male student punished for sexual assault at the University of the South, Sewanee, in Tennessee. But a jury sided with the student on other grounds, agreeing the college failed to provide basic fairness. Sewanee, the jury agreed, allowed a charge to proceed without adequate evidence and gave the accused little more than 24 hours to prepare for a hearing. Also, administrators failed to interview key witnesses, disclose exculpatory evidence, and have adequately trained employees running the process.

Sokolow, who testified on behalf of the accused student (he usually testifies for colleges), called the ruling important because it established that even private colleges can be found negligent if they don’t meet basic standards.

Then there’s the case of Edwin Bleiler, who was expelled from Holy Cross in Massachusetts on the day he was supposed to graduate last spring, for allegedly sexually assaulting another student. The accuser maintained she’d been intoxicated and unable to give consent to a sexual encounter. Bleiler contends she wasn’t incapacitated and acted willingly.

Now, Bleiler is suing Holy Cross, arguing the college’s consent and sexual misconduct policies discriminate against male students — violating his Title IX rights. An attorney for Bleiler, Emily Smith-Lee, contends his Title IX claim is stronger than the one dismissed in the Sewanee case: Bleiler’s case goes beyond the argument that Holy Cross implemented its sexual assault policy in a discriminatorily shoddy fashion. Rather, it claims the policies are inherently tilted against men, by creating different standards for male and female students.

Holy Cross declined to comment.

Russlynn Ali, the assistant secretary who oversees the Department of Education’s Office of Civil Rights, declined to comment on specific cases, and said she did not believe the department had ever received a complaint alleging a male student’s Title IX rights were violated in a sexual assault proceeding. But, if it ever did, the complaint would be looked into.

“Title IX protects all students, male and female, against sex discrimination,” she said.

Wendy Murphy, a Boston attorney and victims’ advocate who has filed numerous Title IX complaints on behalf of victims, says colleges cave too easily to the threat of lawsuits from students accused of sexual violence. Most victims don’t have the resources to sue, which is precisely why they depend on campus Title IX procedures to ensure they are protected. That requires putting a thumb on the scale in favor of victims — such as the “preponderance of the evidence” standard the Obama administration has said schools must use in adjudicating such cases.

Colleges must protect victims, she says. That means abandoning the fantasy they can make everybody happy by also offering accused students the full due process rights they’d enjoy in a criminal trial.

“You can’t run a school that way,” Murphy said. “If every once in a while a school has to be sued at the cost of being fair to all students, so be it.”